1-180787752-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PVS1_ModeratePP3_Moderate
The NM_004736.4(XPR1):c.122-1G>C variant causes a splice acceptor change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000443 in 1,580,998 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004736.4 splice_acceptor
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPR1 | NM_004736.4 | c.122-1G>C | splice_acceptor_variant | ENST00000367590.9 | |||
XPR1 | NM_001135669.2 | c.122-1G>C | splice_acceptor_variant | ||||
XPR1 | NM_001328662.2 | c.122-1G>C | splice_acceptor_variant | ||||
XPR1 | NR_137330.2 | n.302-1G>C | splice_acceptor_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPR1 | ENST00000367590.9 | c.122-1G>C | splice_acceptor_variant | 1 | NM_004736.4 | P1 | |||
XPR1 | ENST00000367589.3 | c.122-1G>C | splice_acceptor_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000873 AC: 2AN: 229030Hom.: 0 AF XY: 0.0000161 AC XY: 2AN XY: 124098
GnomAD4 exome AF: 0.00000350 AC: 5AN: 1428912Hom.: 0 Cov.: 29 AF XY: 0.00000563 AC XY: 4AN XY: 709914
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 152086Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74286
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jul 19, 2022 | Canonical splice site variant in a gene or region of a gene for which loss of function is not a well-established mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at